Community-managed, no-take marine reserves are increasingly promoted as a simple, precautionary measure to conserve biodiversity and sustain coral reef fisheries. However, we need to demonstrate the effects of such reserves to those affected by the loss of potential fishing grounds and the wider scientific community. We surveyed changes in fish communities in five small marine reserves in the central Philippines and three distant Control sites over seven years. We conducted underwater visual censuses of 53 fish families within the reserve (Inside), with a kilometre of the boundary (Outside) and at Control sites. We found significant differences between fish communities Inside and Outside the reserve only at the two sites with strictest compliance with fishing prohibition, while there were significant differences to distant Control sites in all cases. The strongest responses to reserve protection were found in predatory fishes (groupers and breams) and in butterflyfish. Other abundant fish families showed weak effects of protection. For all taxa analysed, we found significant effects of reserve Site and Site × Treatment interactions. The detection of fish responses to reserves is complicated by potential spillover effects, site-specific factors, particularly compliance, and the difficulty of identifying appropriate control areas.